Suchergebnisse

Synthetic Biology (SB) is a revolutionary discipline with a vast range of practical applications, but is SB research really based on engineering principles? Does it contributing to the artificial synthesis of life or does it utilise approaches sufficiently advanced to fall outside the scope of biotechnology or metabolic engineering? This volume reviews the development of SB and includes the major milestones of the discipline, the 'top-down' and 'bottom-up' approaches towards the construction of an artificial cell and the development of the 'iGEM' competition. We conclude that SB is an emerging field with extraordinary technological potential, but that most research projects actually are an extension of metabolic engineering since the complexity of living organisms, their tight dependence on evolution and our limited knowledge of the interactions between the molecules, actually make life difficult to engineer.

The concept of standard strongly evokes machines, industries, electric or mechanical devices, vehicles, or furniture. Indeed, our technological civilization would not be possible – at least in the terms it is structured today – without universal, reliable components, whose acknowledged use results in competitive costs, robustness and interchangeability. For example, an Ikea screw can be used in a wide set of structurally dissimilar furniture and an app can be run on many different smartphones. The very concept of standardization is linked to the industrial revolution and mass production of goods through assembly lines. The question we will try to answer in the present paper is the extent to which standards and the standardization process can be accomplished in the biological realm. ; The authors' work is funded by the Ministry of Science and Innovation and ERDF (RTI2018-095584-B-C41) and the European Union H2020 (BioRobooST: Fostering synthetic biology standardization through international collaboration, Project ID 210491758). ; Peer reviewed

Synthetic biology is the engineering view on biotechnology that ultimately aims at fulfilling the quest of building an artificial cell. From the very first attempts of synthesizing life, this subject has made an impact on the media through, very often, misleading headlines and news. We review here the historical journalistic approach on synthetic biology and related disciplines, from the early twentieth century to the lastest achievements on designing protocells or genome reduction. However, it would be very naive to consider the research community and the media to be unidirectionally linked, with the latter being mere displayers (and disrupters) of the research "reality". On the contrary, the research community has also received a strong influence from the media, as evidenced by statements from researchers, common metaphors and, even, a trend to unconsciously develop shared techno-social paradigms. We conclude that, beyond overstatements from researchers and journalists' misunderstandings, both communities provide strong feedback to each other and, together, contribute to define the dream that synthetic biologists are aiming for. ; The laboratory work of both authors is supported in part by the Spanish Government (Helios, grant reference: BIO2015–66960-C3–1-R co-financed by FEDER funds and Ministerio de Economía y Competitividad) and by the European Union through the BioRoboost project, H2020-NMBP-TR-IND-2018-2020/BIOTEC-01-2018 (CSA), Project ID 210491758. ; Peer reviewed

The largest survey on the perception of synthetic biology‐related disciplines (Porcar et al., 2019,EMBO Rep 20) recently revealed that the Spanish society does not have a very positive perception of the term synthetic biology. On the other hand, the terms biotechnology and even genetic engineering received relatively higher scores. The issue of nomenclature and perception is a classical one in science perception studies. Synthetic biologists have been debating their neologism (Synthetic Biology, from now on SB) for years. Even in a 2006 blog, Rob Carlson discussed the various labels for the new field, such as intentional biology, constructive biology, natural engineering, synthetic genomics and biological engineering. This diversity of names, along with the above mentioned negative public perception of the term synthetic biology, raises the question on whether the term itself is suitable or whether it could, in an extreme scenario, be replaced by another combining scientific consensus with public acceptance. ; This work was funded by the European Union through the BioRoboost project, H2020‐NMBP‐TR‐IND‐2018‐2020/BIOTEC‐01‐2018 (CSA), Project ID 210491758. ; Peer reviewed

Commercial table salt is a condiment with food preservative properties by decreasing water activity and increasing osmotic pressure. Salt is also a source of halophilic bacteria and archaea. In the present research, the diversity of halotolerant and halophilic microorganisms was studied in six commercial table salts by culture-dependent and culture-independent techniques. Three table salts were obtained from marine origins: Atlantic Ocean, Mediterranean (Ibiza Island), and Odiel marshes (supermarket marine salt). Other salts supplemented with mineral and nutritional ingredients were also used: Himalayan pink, Hawaiian black, and one with dried vegetables known as Viking salt. The results of 16S rRNA gene sequencing reveal that the salts from marine origins display a similar archaeal taxonomy, but with significant variations among genera. Archaeal taxa Halorubrum, Halobacterium, Hallobellus, Natronomonas, Haloplanus, Halonotius, Halomarina, and Haloarcula were prevalent in those three marine salts. Furthermore, the most abundant archaeal genera present in all salts were Natronomonas, Halolamina, Halonotius, Halapricum, Halobacterium, Haloarcula, and uncultured Halobacterales. Sulfitobacter sp. was the most frequent bacteria, represented almost in all salts. Other genera such as Bacillus, Enterococcus, and Flavobacterium were the most frequent taxa in the Viking, Himalayan pink, and black salts, respectively. Interestingly, the genus Salinibacter was detected only in marine-originated salts. A collection of 76 halotolerant and halophilic bacterial and haloarchaeal species was set by culturing on different media with a broad range of salinity and nutrient composition. Comparing the results of 16S rRNA gene metataxonomic and culturomics revealed that culturable bacteria Acinetobacter, Aquibacillus, Bacillus, Brevundimonas, Fictibacillus, Gracilibacillus, Halobacillus, Micrococcus, Oceanobacillus, Salibacterium, Salinibacter, Terribacillus, Thalassobacillus, and also Archaea Haloarcula, Halobacterium, and Halorubrum were identified at least in one sample by both methods. Our results show that salts from marine origins are dominated by Archaea, whereas salts from other sources or salt supplemented with ingredients are dominated by bacteria. ; This research was financially supported by the Spanish Government on SETH Project (reference: RTI2018-095584-B-C41-42-43-44, co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades), the Helios project (reference: BIO2015-66960-C3-1-R), and the European CSA on biological standardization BIOROBOOST (EU grant no. 820699). LS was funded by the European project BIOROBOOST. AL-P was funded by Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (reference: DI-17-09613). ; Peer reviewed

Here we show the bacteriome of wasted chewing gums from five different countries and the microbial successions on wasted gums during three months of outdoors exposure. In addition, a collection of bacterial strains from wasted gums was set, and the biodegradation capability of different gum ingredients by the isolates was tested. Our results reveal that the oral microbiota present in gums after being chewed, characterised by the presence of species such as Streptococcus spp. or Corynebacterium spp., evolves in a few weeks to an environmental bacteriome characterised by the presence of Acinetobacter spp., Sphingomonas spp. and Pseudomonas spp. Wasted chewing gums collected worldwide contain a typical sub-aerial biofilm bacteriome, characterised by species such as Sphingomonas spp., Kocuria spp., Deinococcus spp. and Blastococcus spp. Our findings have implications for a wide range of disciplines, including forensics, contagious disease control, or bioremediation of wasted chewing gum residues. ; Financial support from the Spanish Government on SETH Project (Reference: RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the European CSA on biological standardization BIOROBOOST (EU Grant number 820699) are acknowledged. LS is funded by European project BIOROBOOST. ÀVV is funded with a FPU (Formación de Profesorado Universitario) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578. ; Peer reviewed

The Nagoya Protocol on Access and Benefit-sharing (https://www.cbd.int/abs/), primarily designed for vascular plant and animal resources, is also extended to the use of microbial resources, but its application to the microbiological realm has raised many doubts and provoked criticisms. This is because of the particularities of microbial ecology and the technical and legal difficulties encompassed in its application. ; This work was funded by the European Union through the BioRo-boost Project, H2020-NMBP-TR-IND-2018-2020/BIOTEC-01-2018(CSA), Project ID 820699. ; Peer reviewed

Financial support from the European CSA on biological standardization BIOROBOOST (EU grant number 820699, http://standardsinsynbio.eu) is acknowledged. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. ALP is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐17‐09613. ; Peer reviewed

This article belongs to the Section Environmental Microbiology. ; Three novel Gram-positive, aerobic, chemoheterotrophic, motile, non-endospore-forming, orange-pigmented bacteria designated strains T13T, T90T and R8T were isolated from the Tabernas Desert biocrust (Almería, Spain). Cells of the three strains were coccus-shaped and occurred singly, in pairs or clusters. The three strains were oxidase-negative and catalase-positive, and showed a mesophilic, neutrophilic and non-halophilic metabolism. Based on the 16S rRNA gene sequences, the closest neighbours of strains T13T, T90T and R8T were Kineococcus aurantiacus IFO 15268T, Kineococcus gypseus YIM 121300T and Kineococcus radiotolerans SRS 30216T (98.5%, 97.1% and 97.9% gene sequence similarity, respectively). The genomes were sequenced, and have been deposited in the GenBank/EMBL/DDBJ databases under the accession numbers JAAALL000000000, JAAALM000000000 and JAAALN000000000, respectively, for strains T13T, T90T and R8T. The average nucleotide identity (ANIb) and digital DNA-DNA hybridization (dDDH) values confirmed their adscription to three new species within the genus Kineococcus. The genomic G + C content of strains T13T, T90T and R8T ranged from 75.1% to 76.3%. The predominant fatty acid of all three strains was anteiso-C15:0. According to a polyphasic study, strains T13T, T90T and R8T are representatives of three new species in the genus Kineococcus, for which names Kineococcus vitellinus sp. nov. (type strain T13T = CECT 9936T = DSM 110024T), Kineococcus indalonis sp. nov. (type strain T90T = CECT 9938T = DSM 110026T) and Kineococcus siccus sp. nov. (type strain R8T = CECT 9937T = DSM 110025T) are proposed. ; Financial support from Spanish Government (Grant HELIOS with reference: BIO2015-66960-C3-1-R; and grant SETH with reference RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) is acknowledged. EMM is a recipient of a Formación del Profesorado Universitario (FPU) grant with reference FPU17/04184, from the Ministerio de Ciencia, Innovación y Universidades (Spain). ; Peer reviewed

Microbial communities from harsh environments hold great promise as sources of biotechnologically relevant strains and compounds. In the present work, we have characterized the microorganisms from the supralittoral and splash zone in three different rocky locations of the Western Mediterranean coast, a tough environment characterized by high levels of irradiation and large temperature and salinity fluctuations. We have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. All three locations displayed very similar taxonomic profiles, with the genus Rubrobacter and the families Xenococcaceae, Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa; and Ascomycota and halotolerant archaea as members of the eukaryotic and archaeal community respectively. In parallel, the culture‐dependent approach yielded a 100‐isolates collection, out of which 12 displayed high antioxidant activities, as evidenced by two in vitro (hydrogen peroxide and DPPH) and confirmed in vivo with Caenorhabditis elegans assays, in which two isolates, CR22 and CR24, resulted in extended survival rates of the nematodes. This work is the first complete characterization of the Mediterranean splash‐zone coastal microbiome, and our results indicate that this microbial niche is home of an extremophilic community that holds biotechnological potential. ; Financial support from the Spanish Government (Grant Helios, Reference: BIO2015‐66960‐C3‐1‐R co‐financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) and from the European CSA on biological standardization BIOROBOOST (EU grant number 820699) is acknowledged. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐16‐08976. ÀVV is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578. ; Peer reviewed

Bioprospecting expeditions are often performed in remote locations, in order to access previously unexplored samples. Nevertheless, the actual potential of those samples is only assessed once scientists are back in the laboratory, where a time-consuming screening must take place. This work evaluates the suitability of using Nanopore sequencing during a journey to the Tabernas Desert (Spain) for forecasting the potential of specific samples in terms of bacterial diversity and prevalence of radiation- and desiccation-resistant taxa, which were the target of the bioprospecting activities. Samples collected during the first day were analyzed through 16S rRNA gene sequencing using a mobile laboratory. Results enabled the identification of locations showing the greatest and the least potential, and a second, informed sampling was performed focusing on those sites. After finishing the expedition, a culture collection of 166 strains belonging to 50 different genera was established. Overall, Nanopore and culturing data correlated well, since samples holding a greater potential at the microbiome level also yielded a more interesting set of microbial isolates, whereas samples showing less biodiversity resulted in a reduced (and redundant) set of culturable bacteria. Thus, we anticipate that portable sequencers hold potential as key, easy-to-use tools for in situ-informed bioprospecting strategies. ; Financial support from the Spanish Government grant SETH (ref: RTI2018-095584-B-C41-42-43-44) is acknowledged. AL-P is a recipient of a Doctorado Industrial fellowship from the Spanish Ministerio de Ciencia, Innovación y Universidades (reference DI-17-09613). ; Peer reviewed

Here, we present the genome sequence and annotation of the novel bacterial strain HV4-5-C5C, which may represent a new genus within the family Oscillospiraceae (order Eubacteriales). This strain is a potential keystone species in the hydrolysis of complex polymers during anaerobic digestion of biomass. ; We acknowledge funding by the European Union through the BioRoboost project, H2020-NMBP-TR-IND-2018-2020/BIOTEC-01-2018 (Coordination and Support Action), project ID 210491758. This study was also funded by the German Federal Ministry of Economic Affairs and Energy (grant numbers KF 2050830SA4, KF 3400701SA4, and KF 2112205SA4). Finally, we are grateful for open access funding by the publication fund of the Technische Universität Dresden. ; Peer reviewed

Two novel Gram-staining-negative, aerobic, cocci-shaped, non-motile, non-spore forming, pink-pigmented bacteria designated strains T6T and T18T, were isolated from a biocrust (biological soil crust) sample from the vicinity of the Tabernas Desert (Spain). Both strains were catalase-positive and oxidase-negative, and grew under mesophilic, neutrophilic and non-halophilic conditions. According to the 16S rRNA gene sequences, strains T6T and T18T showed similarities with Belnapia rosea CGMCC 1.10758T and Belnapia moabensis CP2CT (98.11 and 98.55% gene sequence similarity, respectively). The DNA G+C content was 69.80 and 68.96% for strains T6T and T18T, respectively; the average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) values confirmed their adscription to two novel species within the genus Belnapia. The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C16 : 0, C18 : 1 2-OH and summed feature 3 (C16 : 1ω7c/C16 : 1ω6c). According to he results of the polyphasic study, strains T6T and T18T represent two novel species in the genus Belnapia (which currently includes only three species), for which names Belnapia mucosa sp. nov. (type strain T6T = CECT 30228T=DSM 112073T) and Belnapia arida sp. nov. (type strain T18T=CECT 30229T=DSM 112074T) are proposed, respectively. ; Financial support from Spanish Government (Grant SETH with reference RTI2018-095584-B-C41-42-43-44 co-financed by FEDER funds and Ministerio de Ciencia, Innovación y Universidades) is acknowledged. E.M.M. and À.V.V. are recipients of a Formación del Profesorado Universitario (FPU) grant with references FPU17/04184 and FPU18/02578, respectively, from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades, Spain). ; Peer reviewed

Solar panel surfaces can be colonized by microorganisms adapted to desiccation, temperature fluctuations and solar radiation. Although the taxonomic and functional composition of these communities has been studied, the microbial colonization process remains unclear. In the present work, we have monitored this microbial colonization process during 24 months by performing weekly measurements of the photovoltaic efficiency, carrying out 16S rRNA gene high‐throughput sequencing, and studying the effect of antimicrobial compounds on the composition of the microbial biocenosis. This is the first time a long‐term study of the colonization process of solar panels has been performed, and our results reveal that species richness and biodiversity exhibit seasonal fluctuations and that there is a trend towards an increase or decrease of specialist (solar panel‐adapted) and generalist taxa, respectively. On the former, extremophilic bacterial genera Deinococcus, Hymenobacter and Roseomonas and fungal Neocatenulostroma, Symmetrospora and Sporobolomyces tended to dominate the biocenosis; whereas Lactobacillus sp or Stemphyllium exhibited a decreasing trend. This profile was deeply altered by washing the panels with chemical agents (Virkon), but this did not lead to an increase of the solar panels efficiency. Our results show that solar panels are extreme environments that force the selection of a particular microbial community. ; Financial support from the Spanish Government (grant Helios. reference: BIO2015‐66960‐C3‐1‐R co‐financed by FEDER funds and Ministerio de Economía y Competitividad) and from the European CSA on biological standardization BIOROBOOST (EU grant number 820699) are acknowledged. KT is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐16‐08976. AL is a recipient of a Doctorado Industrial fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference DI‐17‐09613. EMM is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU17/04184. AVV is funded with a Formación de Profesorado Universitario (FPU) grant from the Spanish Government (Ministerio de Ciencia, Innovación y Universidades), with reference FPU18/02578. CV is a recipient of a Torres Quevedo fellowship from the Ministerio de Ciencia, Innovación y Universidades (Spain), with reference PTQ‐16‐08227. ; Peer reviewed